Vocabulary Administration Overview

A set of administrative shell scripts are provided to manage the LexEVS Service. These scripts are provided for Windows (.bat) and Linux (.sh) operating systems and call wrapper classes for LexEVS administration API classes. These scripts are located in the {LEXBIG_DIRECTORY}/admin and {LEXBIG_DIRECTORY}/test directory. A full description of the options with an example is provided for each command line script.

If you are loading a large vocabulary such as SNOMED or the NCI Metathesaurus, then we recommend the use of these scripts over the GUI since adjusting system memory requirements can be accomplished by changing the load script with a text editor.

Coding Scheme Metadata Access and Administration

Options:
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
f,-force Force activation (no confirmation).

Example:
ActivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" |

Options:
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
d,-date <yyyy-MM-dd,HH:mm:ss> Date and time for deactivation to take effect; immediate if not specified.
f,-force Force deactivation (no confirmation).

Example:
DeactivateScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -d "01/31/2099,12:00:00 |

Options:
a,-all List all extensions (default, override by specifying other options).
i,-index List index extensions.
m,-match List match algorithm extensions.
s,-sort List sort algorithm extensions.
g,-generic List generic extensions.

Example:
ListExtensions --a |

Example:
ListSchemes |

Options:
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
t,-tag The tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Example:
TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v 05.09e" -t "TEST" |

Lucene Index Administration

Options:

-h, --help, Prints usage information

r,-reindex, Reindex any missing indicies.

Note: Lucene Clean Up can only be executed in the default Single Index Mode.

Example:

CleanUPLuceneIndex -r |

Optimizes the Common Lucene Index. |

Options:
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
i,-index <name> Name of the index extension to rebuild (if absent, rebuilds all built-in indices and named extensions).
f,-force Force clear (no confirmation).

Example:
RebuildIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" -i "myindex" |

Options
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
i,-index <name> Name of the index extension to clear.
f,-force Force clear (no confirmation).

Example: RemoveIndex -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" |

Misc Data Base Administration Scripts

Argument:
p,-password password for encryption.

Example: PasswordEncryptor -p lexgrid |

LexEVS Export Scripts

usage: ExportLgXML [VKC:-xc] [VKC:-an null] [VKC:-xall] -v null -u name -out uri [VKC:-xa] [VKC:-f]
an,-associationsName Export associations with this name. Only valid with export type 'xa'
f,-force If specified, allows the destination file to be overwritten if present.
out,-output <uri> URI or path of the directory to contain the resulting XML file. The file name will be automatically derived from the coding scheme name.
u,-urn <name> URN or local name of the coding scheme to export.
v,-version The assigned tag/label or absolute version identifier of the coding scheme.
xa,-exportAssociationsType of export: export only associations.
xall,-exportAll Type of export: export all content. Default behavior.
xc,-exportConcepts Type of export: export only concepts.

Example:
ExportLgXML -out "file:///path/to/dir" -u "NCI Thesaurus" -v "05.06e" -f |

Options:
out,-output <uri> URI or path of the directory to contain the resulting OBO file. The file name will be automatically derived from the coding scheme name.
u,-urn <name> URN or local name of the coding scheme to export.
v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
f,-force If specified, allows the destination file to be overwritten if present.

Note: If the coding scheme and version values are unspecified, a list of available coding schemes will be presented for user selection.

Example: ExportOBO -out "file:///path/to/dir" -nf -f
Example: ExportOBO -out "file:///path/to/dir" -u "FBbt" -v "PRODUCTION" -nf -f |

Options:
out,-output <uri> URI or path of the directory to contain the resulting OWL file. The file name will be automatically derived from the coding scheme name.
u,-urn <name> URN or local name of the coding scheme to export.
v,-version <id> The assigned tag/label or absolute version identifier of the coding scheme.
f,-force If specified, allows the destination file to be overwritten if present.

Note: If the URN and version values are unspecified, a list of available coding schemes will be presented for user selection.

Example: ExportOwlRdf -out "file:///path/to/dir" -f
Example: ExportOwlRdf -out "file:///path/to/dir" -u "sample" -v "1.0" -f |

LexEVS Loader Scripts

Options:
in,-input <uri> URI specifying location of the source file.
-v, --validate <level> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify document is well-formed
1 = Verify document is valid
nf,-noFail If specified, indicates that processing should not stop for recoverable errors.
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
-t, --tag <tagID> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Load Example:
LoadLgXML -in "file:///path/to/file.xml" -nf --a

Validation Example:
LoadLgXML -in "file:///path/to/file.xml" -v 0 |

Options:
in,-input <uri> URI specifying location of the history file
vf,-versionFile <uri> URI specifying location of the file containing version identifiers for the history to be loaded.
-v, --validate <level> Perform validation of the candidate resource without loading data. If specified, the '-nf' and '-r' options are ignored. Supported levels of validation include:
0 = Verify top 10 lines are correct format
1 = Verify correct format for the entire file
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-r, --replace If not specified, the provided history file will be added into the current history database; otherwise the current database will be replaced by the new content.

Load Example:
LoadNCIHistory --nf -in "file:///path/to/history.file" --vf "file:///path/to/version.file"

Validation Example:
LoadNCIHistory -in "file:///path/to/history.file" -v 0

Versions File format information:
releaseDate | isLatest | releaseAgency | releaseId | releaseOrder | entityDescription

Sample record:
28-NOV-05 | false | http://nci.nih.gov/ | 05.10e | 26 | Editing of NCI Thesaurus 05.10e was completed on October 31, 2005. Version 05.10e was October's fifth build in our development cycle. |

Loads a file specified in the Open Biomedical Ontologies (OBO) format.

Options:
in,-input <uri> URI or path specifying location of the source file
-v, --validate <int> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify document is valid
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated
-t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Example: LoadOBO -in "file:///path/to/file.obo" -nf -a
LoadOBO -in "file:///path/to/file.obo" -v 0 |

Note: Load of the NCI Thesaurus should be performed via the LoadNCIThesOWL counterpart, since it will allow more precise handling of NCI semantics.

Options:
in,-input <uri> URI or path specifying location of the source file
-v, --validate <int> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify document is well-formed
1 = Verify document is valid
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated
-t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Example: LoadOWL -in "file:///path/to/somefile.owl" -nf -a
LoadOWL -in "file:///path/to/somefile.owl" -v 0 |

Options:
in,-input <uri> URI or path of the directory containing the NLM files
-v, --validate <int> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify the existence of each required file
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated.
-t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
-il --InheritanceLevel <int> If specified, indicates the extent of inherited relationships to import.
0 = none; 1 = all; 2 = all except is_a (default). All direct relationships are imported, regardless of option.

Example: LoadUMLSSemnet -in "file:///path/to/directory/" -nf --a --il 1
LoadUMLSSemnet -in "file:///path/to/directory/" -v 0 |

Options:
in,-input <uri> URI or path specifying location of the source file
-v, --validate <int> Perform validation of the candidate resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify document is well-formed
1 = Verify document is valid
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated
-t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Example: LoadFMA -in "file:///path/to/FMA.pprj" -nf -a
or
LoadFMA -in "file:///path/to/FMA.pprj" -v 0 |

in,-input <uri> URI or path specifying location of the source file
mf,-manifest <uri> URI or path specifying location of the manifest file
lp,-load preferences <uri> URI or path specifying location of the load preferences file
-v, --validate <int> Perform validation of the candidate
resource without loading data. If specified, the '-nf', -a' and '-t' options are ignored. Supported levels of validation include:
0 = Verify document is valid
nf,-noFail If specified, indicates that processing should not stop for recoverable errors
-a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated
-t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.

Example: LoadHL7RIM -in "file:///path/to/file.mdb" -nf -a
or
LoadHL7RIM -in "file:///path/to/file.mdb" -v 0 |

Example: LoadMetadata -in "file:///path/to/file.xml" -nf -o
or
LoadMetadata -in "file:///path/to/file.xml" |

Example: LoadMrMap -inMap "file:///path/to/MRMAP.RRF -inSat "file:///path/to/MRSAT.RRF" |

Special Batch Loading Functions

Options:
in,-input <uri> URI or path of the directory containing the NLM files

Example: LoadMetaBatch -in "file:///path/to/directory/" |

Loads UMLS content, provided as a collection of RRF files in a
single directory. Files may comprise the entire UMLS distribution
or pruned via the MetamorphoSys tool. A complete list of
source vocabularies is available online athttp://www.nlm.nih.gov/research/umls/metaa1.html.

Options:
in,-input <uri> URI or path of the directory containing the NLM files
s,-source vocabularies to load.

Example: LoadUMLSBatch -in "file:///path/to/directory/" -s "PSY" |

Resume a UMLS load. Loads will usually be restartable if they fail due to an
error. The loader will keep all loaded content and restart at the point of failure.

Options:
in,-input <uri> URI or path of the directory containing the NLM files
s,-source vocabulary to resume.
uri,-uri of vocabulary to resume.
version,-version of vocabulary to resume.

Example: ResumeMetaBatch -in "file:///path/to/directory/" -s "PSY" -uri "urn:123.4" -version "2.0" |

Resume a UMLS load. Loads will usually be restartable if they fail due to an
error. The loader will keep all loaded content and restart at the point of failure.

Options:
in,-input <uri> URI or path of the directory containing the NLM files
s,-source vocabulary to resume.
uri,-uri of vocabulary to resume.
version,-version of vocabulary to resume.

Example: ResumeUmlsBatch.sh -in "file:///path/to/directory/" -s "PSY" -uri "urn:123.4" -version "2.0" |

Scheme and Metadata Removal

Options:
u,-urn <urn> URN uniquely identifying the code system.
v,-version <versionId> Version identifier.
f,-force Force deactivation and removal without confirmation.

Example:
RemoveScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" |

Clears optionally loaded metadata associated with the specified coding scheme.

Options
u,-urn <urn> URN uniquely identifying the code system.
v,-version <id> Version identifier.
f,-force Force clear (no confirmation).

Note: If the URN and version values are unspecified, a
list of available coding schemes will be presented for
user selection.

Example: RemoveMetadata
Example: RemoveMetadata -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "05.09e" |

Pick List and Value Set Load Administration

Options:
in,-input <uri> URI or path specifying location of the source file.
-v, --validate <int> Perform validation of the candidate
resource without loading data.
Supported levels of validation include:
0 = Verify document is well-formed
1 = Verify document is valid

Example: LoadPickListDefinition -in "file:///path/to/file.xml" |

Loads Value Set Definition content, provided in LexGrid canonical xml format.

Options:
in,-input <uri> URI or path specifying location of the source file.
-v, --validate <int> Perform validation of the candidate
resource without loading data.
Supported levels of validation include:
0 = Verify document is well-formed
1 = Verify document is valid

Example: LoadValueSetDefinition -in "file:///path/to/file.xml" |

LexEVS Validation Test Script

Note: the LexEVS runtime and database environments must still be configured prior to invoking the test suite. Running any option other than -v will cause a large set of junits to be run

*

Located in

<br><nowiki>#</nowiki> Loads an OWL file. You can provide a manifest file to configure coding scheme
<br><nowiki>#</nowiki> meta data.
<br><nowiki>#</nowiki>
<br><nowiki>#</nowiki> Options:
<br><nowiki>#</nowiki>   -in,--input <uri> URI or path specifying location of the source file
<br><nowiki>#</nowiki>   -mf,--manifest <uri> URI or path specifying location of the manifest file
<br><nowiki>#</nowiki>   -lp,--loaderPrefs<uri> URI or path specifying location of the loader preference file
<br><nowiki>#</nowiki>   -a, --activate ActivateScheme on successful load; if unspecified the
<br><nowiki>#</nowiki>         vocabulary is loaded but not activated.
<br><nowiki>#</nowiki>   -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign.
<br><nowiki>#</nowiki>
<br><nowiki>#</nowiki> Example: LoadOWL -in "file:///path/to/somefile.owl" -a
<br><nowiki>#</nowiki>
<br>java -Xmx3000m -XX:MaxPermSize=256M -cp "../runtime/lbPatch.jar:../runtime/lbRuntime.jar" org.LexGrid.LexBIG.admin.LoadOWL $@

-Xmx:4000m

-XX:MaxPermSize:256m

/examples_*</tt> to go to the example programs. |

Figure 4 - Sample program output for finding properties and associations for a given code.

Figure 4 - Output of example programs using sample vocabulary

Installing NCI vocabularies

NCI Thesaurus vocabulary

This section describes the steps to download and install a full version of the NCI Thesaurus for the LexEVS Service.

border="0"

|

<tt>*_cd

/admin_*</tt>

For Windows installation use the following command

<tt>*_LoadMetaBatch.bat --in "file:///

/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"_*</tt>

For Linux installation use the following command

<tt>*_ResumeMetaBatch.sh --in "file:///

/" -s "NCI Metathesaurus" -uri "urn:oid:2.16.840.1.113883.3.26.1.2" -version "200601"_*</tt> |

NCI History

This section describes the steps to download and install a history file for NCI Thesaurus.

<tt>*_cd

/admin_*</tt>

For Windows installation use the following command

<tt>*_LoadNCIHistory.bat --nf --in "file:///

" --vf "file:///NCI_HISTORY_DIRECTORY}/VersionFile" _*</tt> |

This file has to be provided to the load API on every load because you will need to maintain it in the future as each new release is made. We have created this file that should be valid as of today from the information that we found in the archive folder on your ftp server. You can find this file in the 'resources' directory of the LexEVS install.</tt> |

Deactivating and Removing a Vocabulary

This section describes the steps to deactivate a coding scheme and remove coding scheme from LexEVS Service.

Example:

<tt>TagScheme -u "urn:oid:2.16.840.1.113883.3.26.1.1" -v "10.10d" -t "PRODUCTION"</tt> |

IndexManagement

LexEVS indexes can be manually updated, removed and optimized by users. This is a useful function particularly when metadata, authoring and post processing may have taken place.

Remove Index

Example:

Windows:
<tt>RebuildIndex.bat</tt>

Linux:
<tt>RebuildIndex.sh</tt> |

Value Set and Pick List Loading

[Value Set and Pick List Scripts]